Images of colony growth for 224 Arabidopsis thaliana bacterial strains on 46 carbon sources

This repository contains all data necessary to score colony growth on agar plates using the software tool 'platescan' (github.com/MicrobiologyETHZ/platescan) for the strains presented in Schäfer, Pacheco, et al. The growth of the 224 strains was split into 3 screens. Rounds 1, 2, and half of 3 comprised the core of the screen for all strains, and the second half of 3 comprised the validation set for computing the false discovery rate. The directories containing the images, as well as their corresponding metadata files, are named accordingly: pictures_7dps_screen_*: folders contain pictures of screening plates to assess growth on tested garbon sources. Pictures were taken 7 days after spotting strains on the plates. *_d7_filenames.txt: files link the picture filename to the carbon source that was tested. In addition the screening round and the plate number within the screening round is indicated. strain_metadata_screen*.txt: files indicate the position of the strains on the test plates [row (alphabetical), row (numbered), column (numbered)] and additional comments relevant for analysis (swarmer). Screen_nr and plate_number allow to link data to the corresponding pictures. This repository additionally includes a script to perform downstream processing of the platescan software output, plate_scan_analysis.R. and a file reporting the latescan output values that were manually overwritten due to contamination or poor image quality manual_correction.txt.本仓库包含了配合软件工具platescan（github.com/MicrobiologyETHZ/platescan）对Schäfer、Pacheco等人研究中涉及的菌株开展琼脂平板菌落生长评分所需的全部数据。本次实验共涉及224株菌株，其生长实验被划分为3轮筛选：第1、2轮及第3轮的前半部分构成了所有菌株的筛选核心数据集，而第3轮的后半部分则作为用于计算错误发现率的验证集。 包含图像及其对应元数据文件的目录命名规则如下： pictures_7dps_screen_*：此类文件夹内存储了用于评估受试碳源生长情况的筛选平板图像，图像拍摄于菌株点种平板后的第7天。 *_d7_filenames.txt：此类文件用于建立图像文件名与受试碳源之间的对应关系，同时还标注了筛选轮次以及该轮次内的平板编号。 strain_metadata_screen*.txt：此类文件记录了菌株在测试平板上的位置[行（字母编号）、行（数字编号）、列（数字编号）]，以及分析相关的附加注释（如游动性菌株（swarmer））。通过screen_nr与plate_number字段可将数据与对应图像进行关联。 本仓库还包含了用于对platescan软件输出结果进行下游处理的脚本plate_scan_analysis.R，以及一份记录了因污染或图像质量不佳而被手动覆盖的latescan输出值的文件manual_correction.txt。